Graph4Med

Graph4Med is an open-source tool for visualizing and analysis of a cohort of patients.

You can try a live demo (no password required).

For more information visit the project homepage or read the full paper:

Schäfer, J., Tang, M., Luu, D. et al. Graph4Med: a web application and a graph database for visualizing and analyzing medical databases. BMC Bioinformatics 23, 537 (2022). (https://doi.org/10.1186/s12859-022-05092-0)

Prerequisites

Graph4Med has been tested with the following versions (others might work as well):

Python 3.6+
Neo4j 4.4.4
- Neo4j APOC Library 4.4.0.3
- Neo4j Graph Data Science (GDS) Library 1.8.4
NeoDash 2.0.13

Running Graph4Med

Install/setup a Neo4j instance with default database neo4j. Make sure to install the APOC and GDS plugins matching your Neo4j version and configure a bolt connector.

Clone this repository:

git clone https://github.com/jeschaef/Graph4Med.git

Change into project folder and install requirements:

pip install -r requirements.txt

Configure the environment variables in the .env file according to your setup:

NEO4J_SERVER="localhost:7687"
NEO4J_USER="myusername"
NEO4J_PASSWORD="mypassword"

If you want to populate the Neo4j database with the sample data from this repository, you can execute the demo.py script:

python demo.py

Run NeoDash and connect to your Neo4j database instance. If you populated the database with demo.py script, there will already be one NeoDash dashboard stored in the default database. Otherwise you can load the dashboard file from this repository.

License

This project is licensed under the MIT License. See LICENSE.